https://github.com/biojulia/formatspecimens.jl
Biological file format specimens for testing packages, and functions to assist in testing.
Science Score: 23.0%
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Repository
Biological file format specimens for testing packages, and functions to assist in testing.
Basic Info
- Host: GitHub
- Owner: BioJulia
- License: other
- Language: Julia
- Default Branch: master
- Size: 5.2 MB
Statistics
- Stars: 14
- Watchers: 7
- Forks: 3
- Open Issues: 0
- Releases: 3
Metadata Files
README.md
FormatSpecimens
Bioinformatics is rife with formats and parsers for those formats.
These parsers don't always agree on the definitions of these formats, since many lack any sort of formal standard.
This repository aims to consolidate a collection of format specimens, forming a unified file set for testing software. Testing against the same cases is a first step towards agreeing on the details and edge cases of a format.
Unlike its predecessor BioFmtSpeciments, FormatSpecimens is version controlled and released to a julia package registry, and features a small julia module to assist in unit-testing.
Install
FormatSpecimens is built primarily for BioJulia, and is maintained with compatibility with the BioJulia ecosystem of tools, and BioJulia developers in mind. FormatSpecimens is made available to install through BioJulia's package registry.
Julia by default only watches the "General" package registry, so before you start, you should add the BioJulia package registry.
Start a julia terminal, hit the ] key to enter pkg mode (you should see the
prompt change from julia> to pkg>), then enter the following command:
julia
registry add https://github.com/BioJulia/BioJuliaRegistry.git
After you've added the registry, you can install FormatSpecimens from the julia
REPL. Press ] to enter pkg mode again, and enter the following:
julia
add FormatSpecimens
Organization
This repository consists of a directory for every major format. Directories
contain format specimens along with a file index.toml. This is a
TOML document.
This index.toml contains two arrays, called valid, and invalid. All the
index records for specimen files that are considered valid (i.e. conform to the
format definition) are found in this array.
All the index records for specimen files that are considered invalid (i.e.
violate the format definition in some way) are found in the invalid array.
Every entry in the valid and invalid arrays have the following fields:
- filename Specimen filename (required).
- origin (Optional) The contributor or source from which a specimen was taken.
- tags (Optional) One or more words used to group specimens by shared features.
- comments (Optional) Any additional information that might be of interest.
Really the only field absolutely required to retrieve a file using the
FormatSpecimens julia module is filename, but the other fields are useful to
manipulate lists of specimen files in your unit tests.
Julia Module
To get a list of all valid or invalid file specimens for a given format, you can do the following:
julia
using FormatSpecimens
goodfiles = list_valid_specimens("FASTQ")
badfiles = list_invalid_specimens("FASTQ")
You can test if a specimen in the list has a given tag, or get an attribute like so:
```julia
Test if the first entry in the list of goodfiles has the tag "dna" in it's
list of tags...
hastag(goodfiles[1], "dna")
Get the comments associated with an entry:
comments(goodfiles[1])
Get the full path of a file in the entry:
fp = joinpath(pathofformat("FASTQ"), filename(entry)) ```
You can also use do notation in order to filter the records e.g. to list all the valid FASTA files that are of a DNA sequence you can filter by tag:
julia
gooddnafiles = list_valid_specimens("FASTA") do x
hastag(x, "dna")
end
Owner
- Name: BioJulia
- Login: BioJulia
- Kind: organization
- Website: https://biojulia.dev
- Repositories: 79
- Profile: https://github.com/BioJulia
Bioinformatics and Computational Biology in Julia
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ben J. Ward | b****d@p****m | 18 |
| Jakob Nybo Nissen | j****n@g****m | 5 |
| Ciarán O'Mara | C****a@u****u | 3 |
| Kevin Bonham | k****n@b****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 2
- Total pull requests: 10
- Average time to close issues: 38 minutes
- Average time to close pull requests: 26 days
- Total issue authors: 2
- Total pull request authors: 5
- Average comments per issue: 17.5
- Average comments per pull request: 0.7
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- SabrinaJaye (1)
- JuliaTagBot (1)
Pull Request Authors
- jakobnissen (8)
- CiaranOMara (3)
- apraga (2)
- kescobo (1)
- SabrinaJaye (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- julia 42 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
juliahub.com: FormatSpecimens
Biological file format specimens for testing packages, and functions to assist in testing.
- Documentation: https://docs.juliahub.com/General/FormatSpecimens/stable/
- License: MIT
-
Latest release: 1.3.1
published about 2 years ago